FAQMAA: A framework for automatic quality assessment of multiple sequence alignments

Multiple Sequence Alignments (MSAs) have significant role in the downstream analysis which includes identifying conserved patterns through evolution, functionally important residues, protein secondary and tertiary structure etc. MSAs, thus, have become an active area of research in the domain of bioinformatics. A large number of MSA methods are available but none of them is capable of producing a correct alignment for all situations. Therefore, knowledge of the most accurate MSA method in the initial stage of a biological research work may help in choosing the right MSA method for the right situation. Traditional technique to assess quality of MSA requires a lot of prior work to be completed such as calculation of guide tree, indel parameters, the best protein evolution model and reference alignment. Currently, no bioinformatic tool is available that performs all the prior work on its own. In this article, we present a framework titled 'FAQMAA' and its implementation in Java programming language that automatically assesses quality of a MSA method. FAQMAA has embedded interrelated open source software applications such as lamba.pl which is used to calculate the indel parameters, PortTest for extracting the best protein evolution model, amino acid frequencies and guide tree, INDELible for generating true alignment and finally SuiteMSA for calculating sum of pairs score and column score. FAQMAA does not require from user a guide tree file, indel parameters, the best protein evolution model, amino acid frequencies or even a reference alignment in order to perform its job. All the prior task is performed by the FAQMAA on its own and helps user save time, tiredness and cumbersome. FAQMAA has expedited the process of measuring quality of a MSA method and helped in selecting the right MSA method in the right situation.